Re: [Treebase-devel] [CDAO-discuss] lat/lon in nexml

[Matt <dia...@gm...>]

A coordinate system would be nice. It, or something similar, would be
necessary for structural alignments which predict pairing of
individual sites separated by some number of nucleotides (e.g.
positions 2 and 34 pair).  Many visualization programs also use
co-ordinates on individual nucleotides.

It might be better though to abstract coordinates given context, to
only calculate the "absolute" coordinates on demand. A paired
structure, as above, could be tied together via ids(?), then
translated/transformed to particular coordinates based on the context.

In real life MSAs will be truncated, extended, extracted from,
concatenated  etc. etc., coordinate management could be come a big
overhead.

Matt

On Mon, Feb 15, 2010 at 11:57 AM, Arlin Stoltzfus <sto...@um...> wrote:
> On Feb 12, 2010, at 9:38 AM, Hilmar Lapp wrote:
>
>> CDAOers: what are status and plans for describing the parts of an
>> alignment right now, and is there support, current or planned, for
>> partitions / segments of an alignment?
>
> Right now there is not even a fully worked out concept of sequence,
> only states of characters.  So, in the matrix:
>
> OTU1 TCAAG
> OTU2 TAAAG
>
> there is no "sequence" concept telling us that "T" and "C" in OTU1 are
> sequentially ordered residues.    They are treated just like classical
> character states in that sense.
>
> One way to deal with this is via MAO, the multiple alignment
> ontology.  We developed a mapping between MAO and CDAO last summer
> that might be useful for this.  MAO has a concept of sub-alignments
> that might be useful here.
>
> Also, in CDAO there is a "coordinate system" concept that we intended
> to use to impose a mapping on characters in a sequence.  The concept
> has not been fleshed out yet.
>
> If there is a coordinate system CS1, with "T" and "C" assigned
> coordinates "1" and "2", and another coordinate system CS2 with "A",
> "A", and "G" assigned coordinates "1", "2" and "3", then this would be
> a way to represent that the data from OTU1 come from 2 different
> sequences.
>
> Arlin
>
>
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